o plot(<lm object>) uses a new default 'which = 5'
for the fourth panel when 'which' is not specified.
o The SVN revision number will appear after the date in the
welcome message. The date shown is now the date of the last
change to the sources rather than the date the sources were
prepared.
o is.null(expression()) now returns FALSE. Only NULL gives TRUE
in is.null().
o graphics::xy.coords, xyz.coords and n2mfrow have been moved to
the grDevices name space (to be available for grid as well).
graphics::boxplot.stats, contourLines, nclass.*, and chull
have been moved to the grDevices name space. The C code
underlying chull() has been moved to package grDevices.
o split(x, f), split<-() and unsplit() now by default split by all
levels of a factor f, even when some are empty.
Use split(x, f, drop = TRUE) if you want the old behavior of
dropping empty levels. split() and split<-() are S3 generic
functions with new arguments 'drop' and '...' and all methods now
should have 'drop' and '...' arguments as well.
o The default for 'allowEscapes' in both read.table() and scan()
has been changed to FALSE.
o The default for 'gcFirst' in system.time() is now TRUE.

NEW FEATURES

o .Platform has a new component 'path.sep', the separator used
between paths in environment variables such as PATH and TEXINPUTS.

o anova.mlm() now handles the single-model case.

o Hexadecimal values are now allowed for as.numeric() and
as.integer() on all platforms, and as integer constants in R code.
o attach() now prints an information message when objects are
masked on the search path by or from a newly attached database.
o axis() now returns 'at' positions.
o axis() has a new argument 'hadj' to control horizontal
adjustment of labels.
o axis.Date() and axis.POSIXct() now accept a 'labels' argument
(contributed by Gavin Simpson).
o barplot() now has arguments 'log = ""' and 'add = FALSE'
(as in barplot2() from package 'gplots').
o baseenv() has been added, to return the base environment. This
is currently still NULL, but will change in a future release.
o boxplot() now responds to supplying 'yaxs' (via bxp()).
(Wish of PR#8072.)
o capabilities() has a new component 'NLS'.
o cbind() and rbind() now react to 'deparse.level' = {0,1,2}
(as in another system not unlike R).
o Experimental versions of cbind() and rbind() in methods package,
based on new generic function cbind2(x,y) and rbind2(). This will
allow the equivalent of S4 methods for cbind() and rbind() ---
currently only after an explicit activation call, see ?cbind2.
o New functions cdplot() and spineplot() for conditional density
plots and spine plots or spinograms. Spine plots are now used
instead of bar plots for x-y scatterplots where y is a factor.
o checkDocFiles() in package 'tools' now checks for bad \usage
lines (syntactically invalid R code).
o The nonparametric variants of cor.test() now behave better in
the presence of ties. The "spearman" method uses the asymptotic
approximation in that case, and the "kendall" method likewise,
but adds a correction for ties (this is not necessary in the
Spearman case).
o The X11 dataentry() now has support for X Input Methods
(contributed by Ei-ji Nakama).
o density() is now an S3 generic where density.default() {former
density()} has new argument 'weights' for specifying observation
masses different than the default 1/N -- based on a suggestion and
code from Adrian Baddeley.
o download.packages() now carries on if it encounters a download
error (e.g. a repository with a corrupt index).
o dump() now skips missing objects with a warning rather than
throw an error.

o Added "POSIXlt" methods for duplicated() and unique().

o Function encoded_text_to_latex() in package tools translates
Latin 1,2,9 and UTF-8 encoded character vectors to LaTeX
escape sequences where appropriate.
o encodeString() allows justify = "none" for consistency with
format.default(). Some argument names have been lengthened
for clarity.
o file(), fifo() and pipe() now (if possible) report a reason
if they fail to open a connection.
o format.default() now has a 'width' argument, and 'justify' can
now centre character strings.
format.default() has new arguments 'na.encode' to control
whether NA character strings are encoded (true by default),
and 'scientific' to control the use of fixed/scientific
notation for real/complex numbers.
How format() works on a list is now documented, and uses
arguments consistently with their usage on an atomic vector.
o format.info() now has a 'digits' argument, and is documented
to work for all atomic vectors (it used to work for all but
raw vectors.).
o New function glob2rx() for translating `wildcard' aka `globbing'
to regular expressions.
o There is a new function gregexpr() which generalizes regexpr()
to search for all matches in each of the input strings (not
just the first match).
o [g]sub() now have a 'useBytes' argument like grep() and regexpr().
o [g]sub(perl = TRUE) support \L and \U in the replacement.

o iconv() has been moved from 'utils' to 'base'.

o identify()'s default method has additional arguments 'atpen'
and 'tolerance' (following S).
o KalmanForecast() and KalmanLike() now have an optional argument
fast=FALSE to prevent their arguments being modified.
o Exact p-values are available in ks.test() for the one-sided and
two-sided one-sample Kolmogorov-Smirnov tests.
o labels() now has a method for "dist" objects (replacing that
for names() which was withdrawn in 2.1.0).
o library() now explicitly checks for the existence of
directories in 'lib.loc': this avoids some warning messages.
o loadNamespace(keep.source=) now applies only to that namespace
and not others it might load to satisfy imports: this is now
consistent with library().
o match.arg() has a new argument 'several.ok = FALSE'.
o max.col() has a new argument for non-random behavior in the
case of ties.
o memory.profile() now uses the type names returned by typeof()
and no longer has two unlabelled entries.
o methods() now warns if it appears to have been called on a
non-generic function.
o The default mosaicplot() method by default draws grey boxes.
o nlminb(), similar to that in S-PLUS, added to package 'stats'.
o New algorithm "port" (the nl2sol algorithm available in the
Port library on netlib) added to the nls() function in the
'stats' package.
o object.size() now supports more types, including external
pointers and weak references.
o options() now returns its result in alphabetical order, and is
documented more comprehensively and accurately. (Now all
options used in base R are documented, including
platform-specific ones.)
Some options are now set in the package which makes use of
them (grDevices, stats or utils) if not already set when the
package is loaded.
o New option("OutDec") to set the decimal point for output conversions.
o New option("add.smooth") to add smoothers to a plot, currently
only used by plot.lm().
o pie() has new optional arguments 'clockwise' and 'init.angle'.
o plot.lm() has two new plots (for 'which' = 5 or 6), plotting
residuals or cook distances versus (transformed) leverages - unless
these are constant. Further, the new argument 'add.smooth' adds a
loess smoother to the point plots by default, and 'qqline = TRUE'
adds a qqline() to the normal plot.
The default for 'sub.caption' has been improved for long calls.
o R.home() has been expanded to return the paths to components
(which can as from this version be installed elsewhere).
o readbin() and writeBin() now support raw vectors as well as
filenames and connections.
o read.dcf() can now read gzipped files.
o read.table() now passes 'allowEscapes' to scan().
o sample(x, size, prob, replace = TRUE) now uses a faster
algorithm if there are many reasonably probable values. (This
does mean the results will be different from earlier versions
of R.) The speedup is modest unless 'x' is very large _and_
'prob' is very diffuse so that thousands of distinct values
will be generated with an appreciable frequency.
o scatter.smooth() now works a bit more like other plotting
functions (e.g., accepts a data frame for argument 'x').
Improvements suggested by Kevin Wright.
o signif() on complex numbers now rounds jointly to give the
requested number of digits in the larger component, not
independently for each component.
o New generic function simulate() in the 'stats' package with
methods for some classes of fitted models.
o smooth.spline() has a new argument 'keep.data' which allows to
provide residuals() and fitted() methods for smoothing splines.
o Attempting source(file, chdir=TRUE) with a URL or connection
for 'file' now gives a warning and ignores 'chdir'.
o source() closes its input file after parsing it rather than
after executing the commands, as used to happen prior to
2.1.0. (This is probably only significant on Windows where
the file is locked for a much shorter time.)
o split(), split<-(), unsplit() now have a new argument 'drop = FALSE',
by default not dropping empty levels; this is *not* back compatible.
o sprintf() now supports asterisk `*' width or precision
specification (but not both) as well as `*1$' to `*99$'. Also the
handling of `%' as conversion specification terminator is now
left to the system and doesn't affect following specifications.
o The plot method for stl() now allows the colour of the range
bars to be set (default unchanged at "light gray").
o Added tclServiceMode() function to the tcltk package to allow
updating to be suspended.
o terms.formula() no longer allows '.' in a formula unless there
is a (non-empty) 'data' argument or 'allowDotAsName = TRUE' is
supplied. We have found several cases where 'data' had not
been passed down to terms() and so '.' was interpreted as a
single variable leading to incorrect results.
o New functions trans3d(), the 3D -> 2D utility from persp()'s
example, and extendrange(), both in package 'grDevices'.
o TukeyHSD() now returns p-values adjusted for multiple comparisons
(based on a patch contributed by Fernando Henrique Ferraz P. da Rosa).
o New functions URLencode() and URLdecode(), particularly for use
with file:// URLs. These are used by e.g. browse.env(),
download.file(), download.packages() and various help() print
methods.
o Functions utf8ToInt() and intToUtf8() to work with UTF-8
encoded character strings (irrespective of locale or OS-level
UTF-8 support).
o [dqp]wilcox and wilcox.test work better with one very large sample
size and an extreme first argument.
o write() has a new argument 'sep'.
o write.csv[2] now also support row.names = FALSE.
o The specification of the substitutions done when processing
Renviron files is more liberal: see ?Startup. It now
accepts forms like R_LIBS=${HOME}/Rlibrary:${WORKGRP}/R/lib .
o Added recommendation that packages have an overview man page
<pkg>-package.Rd, and the promptPackage() function to create a
skeleton version.
o Replacement indexing of a data frame by a logical matrix index
containing NAs is allowed in a few more cases, in particular
always when the replacement value has length one.
o Conversion of .Rd files to latex now handles encoding more
comprehensively, including some support for UTF-8.
o The internal regex code has been upgraded to glibc-2.3.5.
Apart from a number of bug fixes, this should be somewhat
faster, especially in UTF-8 locales.
o PCRE has been updated to version 6.2.
o zlib has been updated to version 1.2.3.
o bzip2 has been updated to version 1.0.3.
o Complex arithmetic is now done by C99 complex types where
supported. This is likely to boost performance, but is
subject to the accuracy with which it has been implemented.
o The printing of complex numbers has changed, handling numbers
as a whole rather than in two parts. So both real and
imaginary parts are shown to the same accuracy, with the
'digits' parameter referring to the accuracy of the larger
component, and both components are shown in fixed or
scientific notation (unless one is entirely zero when it is
always shown in fixed notation).
o Error messages from .C() and .Fortran(), and from parsing errors,
are now more informative.
o The date and date-time functions work better with dates more
than 5000 years away from 1970-01-01 (by making dubious
assumptions about the calendar in use).
o There is now a traditional Chinese translation, and a much more
extensive Russian translation.

DEPRECATED & DEFUNCT
o Capability "IEEE754" is defunct.

o loadURL() is defunct: use load(url()).

o delay() is defunct: use delayedAssign() instead.

o The 'CRAN' argument to update.packages(), old.packages(),
new.packages(), download.packages() and install.packages() is
defunct in favour of 'repos'.
o write.table0() is deprecated in favour of the much faster
write.table().
o format.char() is deprecated in favour of format.default().
o R_HOME/etc/Rprofile is no longer looked for if
R_HOME/etc/Rprofile.site does not exist. (This has been
undocumented since R 1.4.0.)
o CRAN.packages() is deprecated in favour of available.packages().
o Rd.sty no longer processes pre-2.0.0 conversions containing \Link.
o The stubs for the defunct device GNOME/gnome have been removed.
o print.matrix() (which has been identical to print.default since
R 1.7.0) has been removed.

INSTALLATION

o LDFLAGS now defaults to -L/usr/local/lib64 on most Linux
64-bit OSes (but not ia64). The use of lib/lib64 can be
overridden by the new variable LIBnn.
o The default installation directory is now ${prefix}/${LIBnn}/R,
/usr/local/lib64/R on most 64-bit Linux OSes and /usr/local/lib/R
elsewhere.
o The places where the doc, include and share directory trees are
installed can be specified independently: see the R-admin manual.
o We now test for wctrans_t, as apparently some broken OSes have
wctrans but not wctrans_t (which is required by the relevant
standards) .
o Any external BLAS found is now tested to see if the complex
routine zdotu works correctly: this provides a compatibility
test of compiler return conventions.
o Installation without NLS is now cleaner, and does not install
any message catalogues.
o src/modules/lapack/dlamc.f is now compiled with -ffloat-store
if f2c/gcc are used, as well as if g77 is used.
o All the Fortran code has been checked to be fully F77
compliant so there are no longer any warnings from F95
compilers such as gfortran.
o The (not-recommended) options --with-system-zlib,
--with-system-bzlib and -with-system-pcre now have 'system' in
the name.
o If a Java runtime environment is detected at configure time
its library path is appended to LD_LIBRARY_PATH or equivalent.
New Java-related variables JAVA_HOME (path to JRE/JDK), JAVA_PROG
(path to Java interpreter), JAVA_LD_PATH (Java library path)
and JAVA_LIBS (flags to link against JNI) are made available
in Makeconf.
o Ei-ji Nakama was contributed a patch for FPU control with the
Intel compilers on ix86 Linux.

MAC OS X INSTALLATION

o --with-blas="-framework vecLib" --with-lapack and
--with-aqua are now the default configure options.
o The default framework version name was changed to not contain
the patch level (i.e. it is now 2.2 instead of 2.2.0). Also
it can be overridden at configure time by setting FW_VERSION
to the desired name.
o The Rmath stand-alone library is now correctly installed inside
the R.framework if R was configured as a framework. In
addition, make install-Rmath-framework will install a
stand-alone Rmath framework in /Library/Frameworks (unless
overridden by RMATH_FRAMEWORK_DIR specifying full framework
path and name including the .framework extension).

PACKAGE INSTALLATION

o The encoding for a packages' 00Index.html is chosen from the
Encoding: field (if any) of the DESCRIPTION file and from the
\encoding{} fields of any Rd files with non-ASCII titles.
If there are conflicts, first-found wins with a warning.
o R_HOME/doc/html/packages.html is now remade by R not Perl code.
This may result in small changes in layout and a change in
encoding (to UTF-8 where supported).
o The return value of new.packages() is now updated for any
packages which may be installed.
o available.packages() will read a compressed PACKAGES.gz file in
preference to PACKAGES if available on the repository: this
will reduce considerably the download time on a dialup connection.
The downloaded information about a repository is cached for the
current R session.
o The information about library trees found by
installed.packages() is cached for the current session, and
updated only if the modification date of the top-level
directory has been changed.
o A data index is now installed for a package with a 'data' dir
but no 'man' dir (even though it will have undocumented data objects).
o contrib.url path for type="mac.binary" has changed from
bin/macosx/<version> to bin/macosx/<arch>/contrib/<version>
where <arch> corresponds to R.version$arch

UTILITIES

o checkFF() used by R CMD check has since R 2.0.0 not reported
missing PACKAGE arguments when testing installed packages with
namespaces. It now
- treats installed and source packages in the same way.
- reports missing arguments unless they are in a function in
the namespace with a useDynLib declaration (as the
appropriate DLL for such calls can be searched for).
o Rd2dvi sets the encoding(s) used appropriately. If UTF-8
encoding is used, latex >= 2003/12/01 is required.
o codoc() allows help files named pkg_name-defunct.Rd to have
undocumented arguments (and not just base-defunct.Rd).

C-LEVEL FACILITIES

o C function massdist() {called from density()} has new argument
'xmass' (= weights).
o Raw vectors passed to .C() are now passed as unsigned char *
rather than as SEXPs. (Wish of Keith Frost, PR#7853)
o The search for symbols in a .C/.Call/... call without a
package argument now searches for an enclosing namespace and
so finds functions defined within functions in a namespace.
o R_max_col() has new (5th) argument '*ties_meth' allowing
non-random behavior in the case of ties.
o The header files have been rationalized: the BLAS routine
LSAME is now declared in BLAS.h not Linpack.h, Applic.h no
longer duplicates routines from Linpack.h, and Applic.h is
divided into API and non-API sections.
o memory.c has been instrumented so that Valgrind can track R's
internal memory management. To use this, configure using
--with-valgrind-instrumentation=level
where level is 1 or 2. Both levels will find more bugs with
gctorture(TRUE). Level 2 makes Valgrind run extremely slowly.
o Some support for raw vectors has been added to Rdefines.h.
o R_BaseEnv has been added, to refer to the base environment.
This is currently equal to R_NilValue, but it will change in
a future release.

BUG FIXES

o %/% has been adjusted to make x == (x %% y) + y * ( x %/% y )
more likely in cases when extended-precision registers were
interfering.
o Operations on POSIXct objects (such as seq(), max() and
subsetting) try harder to preserve time zones and warn if
inconsistent time zones are used.
o as.function.default() no longer asks for a bug report when
given an invalid body. (PR#1880, PR#7535, PR#7702)
o Hershey fonts and grid output (and therefore lattice output)
now rescale correctly in fit-to-window resizing on a Windows
graphics device. Line widths also scale now.
o Plotmath has more support for multibyte characters (contributed
by Ei-ji Nakama).
o The X11() device now hints the window manager so that decorations
appear reliably under e.g. the GNOME WM (contributed
by Ei-ji Nakama).
o Subsetting a matrix or an array as a vector used to attempt to
use the row names to name the result, even though the
array might be longer than the row names. Now this is only
done for 1D arrays when it is done in all cases, even matrix
indexing. (Tidies up after the fix to PR#937.)
o Constants in mathlib are declared 'const static double' to
avoid performance issues with the Intel Itanium compiler.
o The parser checks the format of numeric constants more
thoroughly so for example '123E-' is no longer valid.
o contourLines() no longer requires an open device (used to
start a device unnecessarily). Fix suggested by Barry Rowlingson.
o capabilities() used partial matching but was not documented
to: it no longer does so.
o kernel(1,0) printed wrongly; kernel(<name-string>, *) now returns
a named kernel in all cases; plot(kernel(.),..) is more flexible.
o qgamma(1,s) didn't give +Inf for some s.
o installed.packages() and download.packages() now always
return a matrix as documented, possibly with 0 rows (rather than
a 0-length character vector or NULL).
o Arithmetic operations on data frames no longer coerce the
names to syntatically valid names.
o Units are now properly recycled in grid layouts
when 'widths' or 'heights' are shorter than the number of
columns or rows (PR#8014).
o DF <- data.frame(A=1:2, B=3:4); DF[1, 1:3] <- NULL gave a wrong
error message.
o spline()/spinefun()'s C code had a memory access buglet which
never lead to incorrect results. (PR#8030)
o sum() was promoting logical arguments to double not integer
(as min() and other members of its group do).
o loess() had a bug causing it to occasionally miscalculate
standard errors (PR#7956). Reported by Benjamin Tyner, fixed
by Berwin Turlach.
o library(keep.source=) was ignored if the package had a
namespace (the setting of options("keep.source.pkgs") was
always used).
o hist.POSIXct() and hist.Date() now respect par("xaxt").
o The 'vfont' argument was not supported correctly in title(),
mtext(), and axis(). The 'vfont' argument is superseded by
the par(family=) approach introduced in 2.0.0. This bug-fix
just updates the warning messages and documentation to
properly reflect the new order of things.
o The C-level function PrintGenericVector could overflow if
asked to print a length-1 character vector of several thousand
characters. This could happen when printing a list matrix,
and was fatal up to 2.1.1 and silently truncated in 2.1.1 patched.
o What happened for proc.time() and system.time() on
(Unix-alike) systems which do not support timing was
incorrectly documented. (They both exist but throw an error.)
Further, systen.time() would give an error in its on.exit
expression.
o weighted.residuals() now does sensible things for glm() fits:
in particular it now agrees with an lm() fit for a Gaussian glm()
fit. (PR#7961).
o The 'lm' and 'glm' methods for add1() took the weights and
offset from the original fit, and so gave errors in the
(dubious) usage where the upper scope resulted in a smaller
number of cases to fit (e.g. by omitting missing values in new
variables). (PR#8049)
o demo() had a 'device' argument that did nothing (although it
was documented to): it has been removed.
o Setting new levels on a factor dropped all existing
attributes, including class "ordered".
o format.default(justify="none") now by default converts NA
character strings, as the other values always did.
o format.info() often gave a different field width from format()
for character vectors (e.g. including missing values or
non-printable characters).
o axis() now ensures that if 'labels' are supplied as character
strings or expressions then 'at' is also supplied (since the
calculated value for 'at' can change under resizing).
o Defining S4 methods for "[" had resulted in changed behavior of S3
dispatch in a very rare case which no longer happens.
o Fixed segfault when PostScript font loading fails, e.g., when
R is unable to find afm files (reported by Ivo Welch).
o R CMD BATCH <file> now also works when <file> does not end in a
newline on Unix-alike platforms.
o terms.formula() got confused if the 'data' argument was a list with
non-syntactic names.
o prompt() and hence package.skeleton() now produce *.Rd files that
give no errors (but warnings) when not edited, much more often.
o promptClass() and promptMethods() now also escape "%" e.g. in '%*%'
and the latter gives a message about the file written.
o wilcox.test() now warns when conf.level is set higher than
achievable, preventing errors (PR#3666) and incorrect answers
with extremely small sample sizes.
o The default (protection pointer) stack size (the default for
'--max-ppsize') has been increased from 10000 to 50000 in order to
match the increased default options("expressions") (in R 2.1.0).
o The R front-end was expecting --gui=tk not Tk as documented,
and rejecting --gui=X11.
o Rdconv -t latex protected only the first << and >> in a chunk
against conversion to guillemets.
o callNextMethod() and callGeneric() have fixes related to
handling arguments.
o ls.diag() now works for fits with missing data. (PR#8139)
o window.default() had an incorrect tolerance and so sometimes
created too short a series if 'start' or 'end' were zero.
o Some (fairly pointless) cases of reshape left a
temporary id variable in the result (PR#8152)
o R CMD build used 'tar xhf' which is invalid on FreeBSD systems
(and followed tar chf, so there could be no symbolic links in
the tarball).
o Subassignment of length zero vectors to NULL gave garbage
answers. (PR#8157)
o Automatic coercion of raw vectors to lists was missing, so for a
list (or data frame) z, z[["a"]] <- raw_vector did not work
and now does. This also affected DF$a <- raw_vector for a
data frame DF.
o The internal code for commandArgs() was missing PROTECTs.
o The width for strwrap() was used as one less than specified.
o R CMD INSTALL was not cleaning up after an unsuccessful
install of a non-bundle which was not already installed.
--
O__ ---- Peter Dalgaard à¸¸ster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk) FAX: (+45) 35327907
_______________________________________________